1.2.1 dev

CMakeLists.txt

@@ -4,6 +4,8 @@ project(
         HOMEPAGE_URL https://github.com/TravisWheelerLab/ULTRA
 )
 
+set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -g")
+
 # By default we do NOT build the standalone ULTRA library
 option(BUILD_ULTRA_LIB "Also build ULTRA as a standalone library" OFF)
 

src/SequenceWindow.cpp

@@ -102,12 +102,6 @@ void SequenceWindow::CalculateSymbolFrequencies() {
   }
 }
 
-/*
-bool SequenceWindow::operator<(const SequenceWindow& rhs) {
-    if (this->seqID != rhs.seqID)
-        return this->seqID < rhs.readID;
-    return (this->readID < rhs.readID);
-}*/
 
 SequenceWindow::SequenceWindow(unsigned long ml, unsigned long mo) {
 

src/cli.hpp

@@ -5,7 +5,7 @@
 #ifndef ULTRA_CLI_HPP
 #define ULTRA_CLI_HPP
 
-#define ULTRA_VERSION_STRING "1.2.0"
+#define ULTRA_VERSION_STRING "1.2.1"
 #define DEBUG_STRING ""
 #ifdef DEBUG_PRAGMA
 #undef DEBUG_STRING

src/repeat.cpp

@@ -54,7 +54,6 @@ void RepeatRegion::CreateLogo(SequenceWindow *window, UMatrix *matrix) {
            }*/
 
     }
-
     else if (fdesc.type == CT_DELETION) {
       deletions += fdesc.indelNumber;
       bplace += fdesc.indelNumber;
@@ -77,6 +76,9 @@ void RepeatRegion::CreateLogo(SequenceWindow *window, UMatrix *matrix) {
       i += bdesc.indelNumber;
     }
 
+    if (fplace >= windowStart+repeatLength)
+      break;
+
     symbol s = window->seq[fplace];
     symbol sb = window->seq[bplace];
 

src/ultra.cpp

@@ -69,7 +69,6 @@ SequenceWindow *Ultra::GetSequenceWindow(SequenceWindow *seq, uthread *uth) {
     pthread_mutex_lock(&outerLock);
 
   // Check to see if we need to read more sequence first
-
   if (!reader->DoneReadingFile()) {
     if (!reader->IsReading()) {
       if (reader->ReadyWindowsSize() == 0) {

src/ultra.hpp

@@ -74,8 +74,7 @@ class Ultra {
 
   bool storeTraceAndSequence = false;
 
-  std::unordered_map<unsigned long long, std::vector<mregion> *>
-      masks_for_seq{};
+  std::unordered_map<unsigned long long, std::vector<mregion> *> masks_for_seq{};
   std::vector<RepeatRegion *> outRepeats{};
   std::vector<UModel *> models{};